Recent efforts to improve sampling of Brazilian biodiversity have yielded a number of undescribed species of amphisbaenids. Herein, we describe a new species of small, two-pored Amphisbaena from western Brazilian Amazonia. The new species can be distinguished from all congeners by the combination of the following characters: two precloacal pores arranged in a continuous series; snout rounded in lateral and dorsal views; tip of tail rounded; 233–250 body annuli; 20–24 caudal annuli; autotomy sites on caudal annuli 6–9; 10 dorsal and 12–14 ventral segments per annulus at midbody; absence of postmalars; suture between frontals slightly smaller than parietal and nasal sutures; and tail short relative to body length (tail length/body length = 0.10). The new species inhabits the rain forest and small patches of savanna vegetation within the Amazon Forest. A Bayesian analysis based on two mitochondrial (16S and ND2) and three nuclear (cmos, BNDF and RAG1) markers recovered the new species as sister to a clade formed by A. hastata A. cuiabana; however, support for this relationship is low. Genetic divergence between populations from both sides of the middle Madeira River is low.